Hepatitis C Virus (HCV) is a positive sense single-strand RNA virus in the family of flavirividae. HCV is a major cause of chronic liver disease worldwide, and remains one of the most common causes of post-transfusion non-A, non-B hepatitis. Of persons who become infected with HCV, 20-25% may be able to clear the virus after the acute infection, but 75-80% will develop chronic Hepatitis C infection. (See, e.g., preface, Frontiers in Viral Hepatitis, Ed. R. F. Chinazi, J.-P. Sommadossi, and C. M. Rice, p. xi., Elsevier (2003)). This usually results in recurrent and progressively worsening liver inflammation, which often leads to more severe states, such as cirrhosis and hepatocellular carcinoma.
Obtaining information of, and quantifying, the HCV genome can facilitate development of a number of approaches for diagnosing and/or treating HCV infection in patients. Generally, analysis of a relatively long fragment of the HCV genome would provide more sequence information which cannot be obtained from multiple, relatively shorter fragments. However, it generally has been difficult to amplify long RNA genomes (e.g., having over 5 kilobases) that require a reverse transcription (RT) step prior to PCR amplification with conventional polymerase chain reactions (PCRs). Such situations are even more challenging when trying to amplify an HCV genome having, for example, greater than 8,000 base pairs, or full-length HCV genome. Also, it has generally been difficult to amplify such a long HCV genome from specimens obtained from clinical and epidemiological studies with relatively high reproducibility.
Therefore, there is a need for new amplification and assay methods of an HCV genome. In particular, there is a need for new amplification and assay methods of an HCV nucleic acid having greater than 8,000 base pairs (e.g., full-length HCV) with relatively high reproducibility (e.g., greater than 80%, greater than 85%, or greater than 90%).